Project Summary/Abstract: Species that are very recently diverged sometimes come back into contact in nature and gener- ate hybrids. This can result in introgression, the movement of genetic material from one species into another. Recent studies of genomic data indicate that introgression is both widespread and an impor- tant source of genetic variation. For example, portions of the human genome trace their ancestry back to Neanderthals or Denisovans, and evidence suggests that some of this introgression was adaptive. Studying patterns of introgression can yield information about population history, selection, and the genes involved in keeping species distinct. One objective of this research is to develop and apply the- oretical models that will aid in the interpretation of patterns of introgression in natural populations. This will contribute to an understanding of how gene flow between species is influenced by selection. This research will be carried out in the Xiphophorus malinche/X. birchmanii species pair, which form large hybrid populations in the wild. Genomic data from these populations will be analyzed to learn more about the process of introgression between the two species. A second objective of this research is to understand the biology of divergence and reproductive iso- lation. This will focus on mapping traits, such as pigmentation, that are different between X. malinche and X. birchmanni. Using genomic data from both wild-caught hybrid individuals and laboratory F2 hybrids, these traits will be mapped to genes. This will contribute to an understanding of how traits such as pigmentation and sword growth are developmentally regulated, as well as an understanding of the process of evolutionary divergence during speciation. The two objectives of this research will be integrated, and together will identify genes that encode traits important for maintaining distinct species, and explicitly describe how selection acts on them in nature.